In a best of 3, he can get out to a hot start and steamroll guys (1st set vs. Delpo in Rotterdam) and finish the match quick. However, in 3 sets, he also can be susceptible to a quick loss, especially if he loses the 1st set. I still don't know how he got out of that Davydenko match last week.

In a best of 5, he can lose a set, maybe go down 2 sets to 1, and still have time to pull it out. But on the flipside, we've seen him in his last few slams win the 1st set (vs. Nadal at AO) or win the first 2 sets (vs. Tsonga at Wimbledon or Djokovic at USO) and see him run out of gas towards the finish line.

Yes I clearly saw him run out-of-gas last year, the most obvious one for me was against Djokovic in the US Open : it was the first time I had seen him red faced, passive, as if he had been hurt by the heat ... which is exactly what happened to Djokovic in the past (please note that I don't say he would have outplayed Djokovic without that : I think first two sets were very tight and Djokovic played better in 3rd set -and end of 2nd set- than in previous sets)

And he's often been used to great starts.

The question imo is more about the past : was it the best-of-5-format which was better for him as many people said or the fact that it was in grand slams then he was better prepared or more motivated ?

He said he felt more comfortable knowing that he could avoid in best-of-5 format the surprises which can happen from lower-ranked players in best-of-3 format :
every high-ranked player could say that, not esp Federer

Also he sometimes showed good stamina in the past (I think of his long match against Nadal in Roma 2006),

but you also know that his record in 5 setter-matches is not great : many explanations have been raised about that, but I wil ask another question : was his stamina that good ? for instance his bad 5th set in Aus open 2009 was it a mental explanation as many people said or could it also be explained by tiredness ?

He hasn't won a best of 5 set match against Nadal in a tennis generation, so that skews things a bit.

True since 2008 , he hasn't beat nadull in a best
Of 5.
However it should also be noted he played nadull once
On a neutral surface & none on an advantageous surface
Wimby-1
USO- 0
Indoor hard BO5 (Davis cup) -0.
So in his natural decline years the battle has been
Fought on his opponents superior surface Clay/high bouncing slow HC outdoors.
To the answer to the question Bo3 me thinks.

(i dont think its physically advisable to play nadal or djokovic in a best of 5)

might sound crazy but running a marathon is worse than doing nothing all day while you drink alcohol, and take drugs and fast food- so you can only imagine what nole and rafa do to their bodies in their matches

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I still think he is better on best of 5 than best of 3, simply best of 3 is easy for upsets and Roger is still one of best player in the world, so as favorit and top player he should be better on best of 5. I don´t think his losses were because of physicall demand-stamina or whatever, his losses when he won 1st serve or was even leading 2sets to love, weren´t losed by stamina-physicallity of those matches. Roger had MP´s against Nole, Tsonga was down 2sets to love, but than he was serving like Ivo at his best and was backing up his serves by huge groundstrokes and net game. Matches againt Rafa are always more mental-match-up issue than stamina-physicall issues. Match against Isner was lost, but Roger was pathetic, Isner great and surface maybe wasn´t best for Roger- for John wasn´t best too of course. Matches on best of 3 Roger can loose matches pretty quick, he lost on clay to Gasquet or Melzer at clay Masters last season. He was beaten by Berdych-in form, he was beaten by Tsonga in Canada and so on, simply best of 3, you need 1 break and serve great and you can win something like 7-6, 6-4 with Roger, so i think Roger is still better at best of 5 format